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Metabolomics Python Packages

Python packages with the GitHub topic metabolomics. Sorted by relevance, with stars and monthly downloads.
OpenMS
pyopenms

The codebase of the OpenMS project

182K 593 429
matchms
matchms

Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.

55K 256 79
microbiomedata
nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

7K 46 10
wfondrie
depthcharge-ms

A deep learning toolkit for mass spectrometry

5K 90 26
aeiwz
metbit

Metabolomics data analysis and visualization tools.

3K 2 0
BiRG
pyopls

A Python 3 implementation of orthogonal projection to latent structures

2K 65 20
metaspace2020
msi-recal

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

2K 57 14
EMSL-Computing
corems

Mass Spectrometry Framework for Small Molecules Analysis

2K 64 39
MetaSys-LISBP
isocor

IsoCor: Isotope Correction for mass spectrometry labeling experiments

2K 24 9
metaspace2020
metaspace2020

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

2K 57 14
lifs-tools
pygoslin

Python implementation for Goslin

1K 4 2
DTUComputeStatisticsAndDataAnalysis
mbpls

(Multiblock) Partial Least Squares Regression for Python

1K 33 8
glasgowcompbio
pymultiomics

Python toolbox for multi-omics data mapping and analysis

989 27 6
Philipbear
msbuddy

Molecular formula annotation for MS-based small molecule analysis.

979 33 6
LewisResearchGroup
ms-mint

Python library for large-scale targeted metabolomics.

963 23 4
MoseleyBioinformaticsLab
mwtab

Parser for mwtab files from the Metabolomics Workbench

942 12 2
AberystwythSystemsBiology
dimepy

Python package for the high-throughput nontargeted metabolite fingerprinting of nominal mass direct injection mass spectrometry.

932 9 3
cbib
dimet

Differential analysis of targeted Isotope-labeled Metabolomics data

917 5 2
mhagar
find-mfs

A Python package for finding molecular formulae candidates which fit some given mass (+/- an error window). Uses Böcker & Lipták's highly efficient algorithm, as implemented in SIRIUS. This package also implements methods for filtering MF candidates by chemical rules, and simulated isotope envelopes.

837 5 1
LewisResearchGroup
ms-mint-app

Metabolomics Integrator Interactive Web-Application (Mint)

719 6 2
phenomecentre
npyc

The nPYc-Toolbox defines objects for representing, and implements functions to manipulate and display, metabolic profiling datasets.

694 25 9
saezlab
omnipath-client

Python client for the new OmniPath web APIs

621 0 0
lucinamay
biosynfoni

a *biosynformatic* fingerprint to explore natural product distance and diversity

590 22 4
cwieder
sspa

Single sample pathway analysis tools for omics data

568 15 6
    • Data from PyPI, GitHub, ClickHouse, and BigQuery